8OK2: DNA replication complex GINS protein PSF1

Name: PDB 8OK2: Bipartite interaction of TOPBP1 with the GINS complex
Published: 2024-03-13
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: replication

Bipartite interaction of TOPBP1 with the GINS complex. Determined by electron microscopy at 4.1 Å resolution. Released 13 Mar 2024.

Method: Electron microscopy
Resolution: 4.1 Å
Organism: Homo sapiens
Chains: 5
Atoms: 7,430
Mol. weight: 147.02 kDa
Released: 13 Mar 2024

Explore 8OK2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8OK2 contains 55 α-helices and 29 β-strands across 5 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	4-15	12
α-helix	17	1
α-helix	22-24	3
α-helix	26-53	28
α-helix	56-58	3
α-helix	59-94	36
α-helix	100-103	4
α-helix	108-127	20

Chain B: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-10	8
β-strand	14-19	6	1
β-strand	23	1	2
α-helix	24-25	2
β-strand	26-28	3	3
β-strand	31-33	3	3
β-strand	36	1	2
β-strand	42-45	4	1
α-helix	46-54	9
β-strand	58-60	3	1
α-helix	61-63	3
α-helix	68-80	13
α-helix	84-87	4
α-helix	92-102	11
α-helix	110-137	28
β-strand	143-144	2	4
α-helix	150-171	22

Chain C: 12 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
α-helix	22-28	7
β-strand	31-36	6	5
β-strand	40	1	6
α-helix	48-50	3
β-strand	60	1	6
β-strand	65-69	5	5
α-helix	70-76	7
β-strand	84-86	3	5
α-helix	90-92	3
α-helix	94-102	9
α-helix	104-106	3
α-helix	109-112	4
α-helix	116-123	8
α-helix	131-155	25
α-helix	162-166	5
α-helix	170-190	21

Chain D: 14 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	23-39	17
α-helix	48-63	16
α-helix	75-102	28
α-helix	104-112	9
α-helix	114-115	2
α-helix	119-120	2
α-helix	124-144	21
α-helix	146-148	3
α-helix	151-153	3
α-helix	158-161	4
α-helix	163-165	3
β-strand	170-175	6	4
β-strand	179-184	6	7
α-helix	190-192	3
β-strand	194-198	5	7
α-helix	199	1
β-strand	203-207	5	4
α-helix	208-217	10
β-strand	220-222	3	4

Chain E: 12 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	485-492	8
β-strand	557-560	4	8
α-helix	565-577	13
β-strand	581-582	2	8
α-helix	583-584	2
β-strand	591-596	6	8
β-strand	607-612	6	8
α-helix	613-622	10
α-helix	628-630	3
α-helix	632-634	3
β-strand	650-653	4	9
α-helix	658-670	13
β-strand	674-675	2	9
β-strand	684	1	10
β-strand	689	1	10
α-helix	690-692	3
β-strand	694-696	3	9
α-helix	703-710	8
β-strand	715-716	2	9
α-helix	718-727	10
α-helix	733-735	3
β-strand	737	1	9
α-helix	738-740	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA replication complex GINS protein PSF1	A	protein	151	Homo sapiens	Q14691 (AlphaFold model)
DNA replication complex GINS protein PSF2	B	protein	185	Homo sapiens	Q9Y248 (AlphaFold model)
DNA replication complex GINS protein PSF3	C	protein	216	Homo sapiens	Q9BRX5 (AlphaFold model)
DNA replication complex GINS protein SLD5	D	protein	262	Homo sapiens	Q9BRT9 (AlphaFold model)
Topoisomerase (DNA) II binding protein 1	E	protein	470	Homo sapiens	Q92547

Sequence of entity 1 (A), FASTA

>8OK2_1 DNA replication complex GINS protein PSF1 (chains A)
MFCEKAMELIRELHRAPEGQLPAFNEDGLRQVLEEMKALYEQNQSDVNEAKSGGRSDLIP
TIKFRHCSLLRNRRCTVAYLYDRLLRIRALRWEYGSILPNALRFHMAAEEMEWFNNYKRS
LATYMRSLGGDEGLDITQDMKPPKSLYIEVR

Sequence of entity 2 (B), FASTA

>8OK2_2 DNA replication complex GINS protein PSF2 (chains B)
MDAAEVEFLAEKELVTIIPNFSLDKIYLIGGDLGPFNPGLPVEVPLWLAINLKQRQKCRL
LPPEWMDVEKLEKMRDHERKEETFTPMPSPYYMELTKLLLNHASDNIPKADEIRTLVKDM
WDTRIAKLRVSADSFVRQQEAHAKLDNLTLMEINTSGTFLTQALNHMYKLRTNLQPLEST
QSQDF

Sequence of entity 3 (C), FASTA

>8OK2_3 DNA replication complex GINS protein PSF3 (chains C)
MSEAYFRVESGALGPEENFLSLDDILMSHEKLPVRTETAMPRLGAFFLERSAGAETDNAV
PQGSKLELPLWLAKGLFDNKRRILSVELPKIYQEGWRTVFSADPNVVDLHKMGPHFYGFG
SQLLHFDSPENADISQSLLQTFIGRFRRIMDSSQNAYNEDTSALVARLDEMERGLFQTGQ
KGLNDFQCWEKGQASQITASNLVQNYKKRKFTDMED

Sequence of entity 4 (D), FASTA

>8OK2_4 DNA replication complex GINS protein SLD5 (chains D)
MHHHHHHGRMDYKDDDDKADYKDDDDKADYKDDDDKGRPMTEEVDFLGQDSDGGSEEVVL
TPAELIERLEQAWMNEKFAPELLESKPEIVECVMEQLEHMEENLRRAKREDLKVSIHQME
MERIRYVLSSYLRCRLMKIEKFFPHVLEKEKTRPEGEPSSLSPEELAFAREFMANTESYL
KNVALKHMPPNLQKVDLFRAVPKPDLDSYVFLRVRERQENILVEPDTDEQRDYVIDLEKG
SQHLIRYKTIAPLVASGAVQLI

Sequence of entity 5 (E), FASTA

>8OK2_5 Topoisomerase (DNA) II binding protein 1 (chains E)
MGSHHHHHHGSLEVLFQGPHMASNSLNSKLEPTLENLENLDVSAFQAPEDLLDGCRIYLC
GFSGRKLDKLRRLINSGGGVRFNQLNEDVTHVIVGDYDDELKQFWNKSAHRPHVVGAKWL
LECFSKGYMLSEEPYIHANYQPVEIPVSHQPESKAALLKKKNSSFSKKDFAPSEKHEQAD
EDLLSQYENGSSTVVEAKTSEARPFNDSTHAEPLNDSTHISLQEENQSSVSHCVPDVSTI
TEEGLFSQKSFLVLGFSNENESNIANIIKENAGKIMSLLSRTVADYAVVPLLGCEVEATV
GEVVTNTWLVTCIDYQTLFDPKSNPLFTPVPVMTGMTPLEDCVISFSQCAGAEKESLTFL
ANLLGASVQEYFVRKSNAKKGMFASTHLILKERGGSKYEAAKKWNLPAVTIAWLLETART
GKRADESHFLIENSTKEERSLETEITNGINLNSDTAEHPRRAWSHPQFEK

Primary citation

TopBP1 utilises a bipartite GINS binding mode to support genome replication. Day, M., Tetik, B., Parlak, M. et al. Nat Commun (2024) 15:1797-1797. DOI 10.1038/s41467-024-45946-0 · PubMed

Other PDB entries of the same protein (UniProt Q14691 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2E9X 2.3 Å, The crystal structure of human GINS core complex
2Q9Q 2.36 Å, The crystal structure of full length human GINS complex
9E2Z 2.6 Å, Cryo-EM structure of human CMG helicase stalled at G4-containing DNA template
7PLO 2.8 Å, H. sapiens replisome-CUL2/LRR1 complex
2EHO 3.0 Å, Crystal structure of human GINS complex
7PFO 3.2 Å, Core human replisome
6XTX 3.29 Å, CryoEM structure of human CMG bound to ATPgammaS and DNA
8B9D 3.4 Å, Human replisome bound by Pol Alpha
6XTY 6.77 Å, CryoEM structure of human CMG bound to AND-1 (CMGA)

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